CGH analyses of human tumors have revealed that chromosomal aberrations result in genomic imbalances specific for different tumor from diverse tissue types. Furthermore, these changes define discrete steps in the progression of epithelial tumors. More than 90% of cervical carcinomas carry extra copies of chromosome 3 and virtually all diploid breast cancers show a gain of chromosome 1q. Also, gains of chromosome 3q precede copy number increases of chromosomes 5p and 1, and loss of chromosome 2 during the genesis of cervical carcinomas. It is therefore conducive to apply the visualization of these recurring and specific chromosomal aberrations to complement and enhance the cytomorphological diagnosis of human cancers and their precursor lesions. This can be achieved using interphase cytogenetics with fluorescently tagged DNA probes that recognize specific chromosomal target regions directly in interphase cells. We have focused on three applications: Identification of the progressive potential of cervical intraepithelial neoplasia based on the detection of extra copies of chromosome 3 and 5 in thinprep PAP-smears. Diagnosis and prognostication of suspicious breast lesions following the detection of chromosomal aneuploidies in fine needle aspirates. Visualization of specific chromosomal aneuploidies in cytokeratin positive epithelial cells isolated from the peripheral blood of breast cancer patients.These projects are accompanied by the improvement of procedures for the preparation of cytological specimens for interphase cytogenetics, by the development of directly labeled, multicolor probe cocktails for relevant chromosomal regions, oncogenes, and tumor suppressor genes (supported by a CRADA with Vysis, Inc.), and by the development of semi-automated or automated microscope hardware and imaging software for fluorescent spot counting. We could show that the visualization of chromosomal aneupoloidies in cytological preparations (fine needle aspirates from the breast and monolayer PAP-smears) is highly specific and sensitive tests for the diagnosis of cancer and premalignant precursor lesions. For instance, the detection of genomic copy number alterations of the human telomerase gene hTERT (which maps to chromosome 3q26) serves as an independent genetic marker for the diagnosis of cervical dysplasia. Other translational research efforts include the use of parallel gene expression profiling for predicting therapy response in rectal carcinomas, and the use of proteomics to identify early markers for the recurrence of colon tumors after surgery.